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Abstract Pyroptosis is a type of programmed cell death characterized by cell swelling and osmotic lysis, resulting in cytomembrane rupture and release of immunostimulatory components, which play a role in several pathological processes. Significant cellular responses to various stimuli involve the formation of inflammasomes, maturation of inflammatory caspases, and caspase-mediated cleavage of gasdermin. The function of pyroptosis in disease is complex but not a simple angelic or demonic role. While inflammatory diseases such as sepsis are associated with uncontrollable pyroptosis, the potent immune response induced by pyroptosis can be exploited as a therapeutic target for anti-tumor therapy. Thus, a comprehensive review of the role of pyroptosis in disease is crucial for further research and clinical translation from bench to bedside. In this review, we summarize the recent advancements in understanding the role of pyroptosis in disease, covering the related development history, molecular mechanisms including canonical, non-canonical, caspase 3/8, and granzyme-mediated pathways, and its regulatory function in health and multiple diseases. Moreover, this review also provides updates on promising therapeutic strategies by applying novel small molecule inhibitors and traditional medicines to regulate pyroptosis. The present dilemmas and future directions in the landscape of pyroptosis are also discussed from a clinical perspective, providing clues for scientists to develop novel drugs targeting pyroptosis.

[Objective] Against the backdrop of tightening incremental land resources, urban development is gradually shifting from relying on the external expansion of incremental land supply to focusing on the intensive model of redevelopment of stock land. This article attempts to explore the impact of incremental land expansion and redevelopment of stock land on urban economic growth at different stages of urban development, in order to provide useful references for the improvement of urban land supply policies. [Methods] Based on the panel data of 284 prefecture level cities from 2009 to 2021 in China, dual fixed effects and threshold effects model were constructed to explore the impact of incremental land expansion and stock land redevelopment on urban economic growth, threshold effects were analyzed at different stages of urban development and scale heterogeneity was analyzed. [Results] (1) The marginal contribution of redevelopment of stock land to economic growth is higher than that of incremental land expansion, and the impact is significant. (2) In the process of urban development, the expansion of incremental land and the redevelopment of existing land both have a population urbanization and per capita GDP threshold effect on urban economic growth. With the continuous improvement of population urbanization and per capita GDP level, the marginal contribution of incremental land expansion to urban economic growth continues to decline, while the marginal contribution of stock land redevelopment to economic growth continues to rise and gradually exceeds that of incremental land expansion. In terms of heterogeneity analysis, the above two threshold effects exist in cities of different scales, and have the same development trend as the national sample. Among them, the threshold value for large cities is higher than the national threshold value, and the national threshold value is higher than the threshold value for small and medium-sized cities. [Conclusion] The traditional externally expanding urban development model relying on incremental land expansion is unsustainable, and cities are gradually entering the era of stock; However, cities of different scales enter the stage of stock development at different times. It is necessary to adopt differentiated land supply strategies for different cities in order to better leverage the driving role of land resources on urban economy.

The coastal Casuarina equisetifolia is the most common tree species in Hainan’s coastal protection forests. Sequencing the genomes of its allelopathic endophytes can allow the protective effects of these bacteria to be effectively implemented in protected forests. The goal of this study was to sequence the whole genomes of the endophytes Bacillus amyloliquefaciens and Bacillus aryabhattai isolated from C. equisetifolia root tissues. The results showed that the genome sizes of B. amyloliquefaciens and B. aryabhattai were 3.854 Mb and 5.508 Mb, respectively. The two strains shared 2514 common gene families while having 1055 and 2406 distinct gene families, respectively. The two strains had 283 and 298 allelochemical synthesis-associated genes, respectively, 255 of which were shared by both strains and 28 and 43 of which were unique to each strain, respectively. The genes were putatively involved in 11 functional pathways, including secondary metabolite biosynthesis, terpene carbon skeleton biosynthesis, biosynthesis of ubiquinone and other terpene quinones, tropane/piperidine and piperidine alkaloids biosynthesis, and phenylpropanoid biosynthesis. NQO1 and entC are known to be involved in the biosynthesis of ubiquinone and other terpenoid quinones, and rfbC/rmlC, rfbA/rmlA/rffH, and rfbB/rmlB/rffG are involved in the biosynthesis of polyketide glycan units. Among the B. aryabhattai-specific allelochemical synthesis-related genes, STE24 is involved in terpene carbon skeleton production, atzF and gdhA in arginine biosynthesis, and TYR in isoquinoline alkaloid biosynthesis. B. amyloliquefaciens and B. aryabhattai share the genes aspB, yhdR, trpA, trpB, and GGPS, which are known to be involved in the synthesis of carotenoids, indole, momilactones, and other allelochemicals. Additionally, these bacteria are involved in allelochemical synthesis via routes such as polyketide sugar unit biosynthesis and isoquinoline alkaloid biosynthesis. This study sheds light on the genetic basis of allelopathy in Bacillus strains associated with C. equisetifolia, highlighting the possible use of these bacteria in sustainable agricultural strategies for weed management and crop protection.

Invasive smooth cordgrass (Spartina alterniflora) has been expanding rapidly through the coastal wetlands of eastern China and these changes negatively affect local birds. In the Dafeng Milu National Nature Reserve (henceforth referred to as DMNNR), rapid degradation of spartina occurs after an increase in milu (Elaphures davidianus; hereafter elk) numbers and ecological hydrological engineering. We evaluated the impact of such degradation on the abundance and species diversity of birds in the DMNNR during 2017–2021. We found that the area covered by S. alterniflora decreased significantly in the study area at a rate of 310 ha per year and by 62% during 2017–2021 (p < 0.01). With this decrease in the S. alterniflora area, the species richness and abundance of birds first increased and then decreased. Songbird density clearly decreased but species richness did not significantly do so. This research demonstrated that during the initial stages of vegetation degradation, there was a positive effect on bird diversity. With the increasing vegetation degradation increases, both songbirds and waterbirds experience negative impacts. The DMNNR is an important stopover site for waterbirds in the East Asian–Australasian Flyway, and additional measures are needed to control vegetation degradation and to restore the native habitats for birds.

Brain natriuretic peptide (BNP) belongs to the family of natriuretic peptides, which are responsible for a wide range of actions. Diabetic cardiomyopathy (DCM) is often associated with increased BNP levels. This present research intends to explore the role of BNP in the development of DCM and the underlying mechanisms. Diabetes was induced in mice using streptozotocin (STZ). Primary neonatal cardiomyocytes were treated with high glucose. It was found that the levels of plasma BNP started to increase at 8 weeks after diabetes, which preceded the development of DCM. Addition of exogenous BNP promoted Opa1-mediated mitochondrial fusion, inhibited mitochondrial oxidative stress, preserved mitochondrial respiratory capacity and prevented the development of DCM, while knockdown of endogenous BNP exacerbated mitochondrial dysfunction and accelerated DCM. Opa1 knockdown attenuated the aforementioned protective action of BNP both in vivo and in vitro. BNP-induced mitochondrial fusion requires the activation of STAT3, which facilitated Opa1 transcription by binding to its promoter regions. PKG, a crucial signaling biomolecule in the BNP signaling pathway, interacted with STAT3 and induced its activation. Knockdown of NPRA (the receptor of BNP) or PKG blunted the promoting effect of BNP on STAT3 phosphorylation and Opa1-mediated mitochondrial fusion. The results of this study demonstrate for the first time that there is a rise in BNP during the early stages of DCM as a compensatory protection mechanism. BNP is a novel mitochondrial fusion activator in protecting against hyperglycemia-induced mitochondrial oxidative injury and DCM through the activation of NPRA-PKG-STAT3-Opa1 signaling pathway.

The gradually increasing presence of arsenic, a highly toxic heavy metal, poses a significant threat to both soil environmental safety and human health. Pteris vittata has long been recognized as an efficient hyperaccumulator plant for arsenic pollution. However, the pattern of arsenic accumulation in soil impacts its bioavailability and restricts the extraction efficiency of Pteris vittata. To address this issue, microorganisms have the potential to improve the arsenic accumulation efficiency of Pteris vittata. In this work, we employed anthropogenic enrichment methods to extract functional iron–sulfur-reducing bacteria from soil as a raw material. These bacteria were then utilized to assist Pteris vittata in the phytoremediation of arsenic-contaminated soil. Furthermore, the utilization of organic fertilizer produced from fermented crop straw significantly boosted the remediation effect. This led to an increase in the accumulation efficiency of arsenic by Pteris vittata by 87.56%, while simultaneously reducing the content of available arsenic in the soil by 98.36%. Finally, the experimental phenomena were studied through a soil-microbial batch leaching test and plant potting test. And the mechanism of the microorganism-catalyzed soil iron–sulfur geochemical cycle on arsenic release and transformation in soil as well as the extraction effect of Pteris vittata were systematically investigated using ICP, BCR sequential extraction and XPS analysis. The results demonstrated that using iron–sulfur-reducing microorganisms to enhance the phytoremediation effect is an effective strategy in the field of ecological restoration.

This paper aims to evaluate the severities and causes of ground surface building and cropland damages after coal mining in a better way, and to clarify the correlation between the damage assessment indexes that influence mining. Against the backdrop of multi-seam mining in certain coal mines in China, the estimated results of each displacement and deformation were analyzed using GIS technology. The damage range determined for each deformation index is divided according to the displacement and deformation combined with the virtue of damage judgment threshold. The damage ranges on the ground surface based on the comprehensive value of each displacement and deformation index were obtained through superimposing those ranges delineated by each displacement and deformation index, and the law on influence from displacement indexes upon various levels of damage was analyzed in a quantitative manner accordingly. The results showed that coal mining destroyed 14 buildings and a cropland area of 11.96 hm2; among them, building damage was only associated with displacement indexes E (horizontal deformation) and T (inclined deformation). Seven buildings were solely destroyed by T alone; five buildings were solely damaged by E; two buildings were damaged jointly by E and T; and, moreover, with the aggravation in building damage level, the proportion of building damage due to E decreased while the proportion of building damage under the same level due to T increased. Regarding cropland destruction, the damage due to T accounted for 33.48% while the damage jointly caused by W (Subsidence), E and T accounted for 30.45%. Moreover, the proportion of damaged cropland area due to inclined deformation T was positively correlated with cropland damage level. These findings can provide a reference for rational judgment regarding civilian building and cropland destruction on the ground surface after coal mining.

How cells control gene expression is a fundamental question. The relative contribution of protein-level and RNA-level regulation to this process remains unclear. Here, we perform a proteogenomic analysis of tumors and untransformed cells containing somatic copy number alterations (SCNAs). By revealing how cells regulate RNA and protein abundances of genes with SCNAs, we provide insights into the rules of gene regulation. Protein complex genes have a strong protein-level regulation while non-complex genes have a strong RNA-level regulation. Notable exceptions are plasma membrane protein complex genes, which show a weak protein-level regulation and a stronger RNA-level regulation. Strikingly, we find a strong negative association between the degree of RNA-level and protein-level regulation across genes and cellular pathways. Moreover, genes participating in the same pathway show a similar degree of RNA- and protein-level regulation. Pathways including translation, splicing, RNA processing, and mitochondrial function show a stronger protein-level regulation while cell adhesion and migration pathways show a stronger RNA-level regulation. These results suggest that the evolution of gene regulation is shaped by functional constraints and that many cellular pathways tend to evolve one predominant mechanism of gene regulation at the protein level or at the RNA level.

Background ET-26 hydrochloride (ET-26HCl) is a novel analogue of etomidate approved for clinical trials. However, all results from recent studies were accomplished in young adult animals. The objective of this study was to evaluate the efficacy and safety of ET-26HCl in aged rats. Methods Aged Sprague-Dawley rats were randomly divided into three groups (three males and three females in each group) were given dose of two-fold of median effective dose (ED50) of ET-26HCl, etomidate and propofol: the measurements of loss of the righting reflex (LORR) and cardiovascular and respiratory function after injection at the two-fold dose of the median effective dose were used for evaluation of effectiveness and safety, and the modified adrenocorticotropic hormone-stimulation experiment was used to evaluate the inhibition effect of the drugs on the synthesis of adrenal cortical hormones. Results There was no significant difference in the onset time among propofol, etomidate and ET-26HCl. The duration of propofol (850.5 ± 77.4 s) was significantly longer than that caused by etomidate (489.8 ± 77.0 s, p = 0.007) and ET-26HCl (347.3 ± 49.0 s, p = 0.0004). No significant difference was observed in the time to stand and normal activity among drugs. A total of 66.7% of rats in the ET-26HCl group were evaluated to have mild hematuria. Then, etomidate and ET-26HCl had a milder blood pressure inhibition effect than propofol. Apnea was observed in all rats administered propofol and the duration for this side effect was 45.0 ± 9.0 s. For etomidate and ET-26HCl, no apnea was observed. No other clinical signs of side-effect were observed, and no rats died. No significant difference was observed in corticosterone concentrations between ET-26HCl and solvent group. However, rats administered etomidate had lower corticosterone concentrations than those administered ET-26HCl at 15, 30, and 60 min. Conclusions Our results indicate ET-26HCl in aged rats is an effective sedative-hypnotic with stable myocardial and respiratory performance and also have mild adrenocortical suppression. Thus, these findings increase the potential for the clinical use of ET-26HCl in the elderly population.

The development of phytoremediation technology is constrained by gentle phytoextraction efficiency and slow biomass accumulation. In this study, a combined remediation of pioneer plants and solid waste towards Cd- and As-contaminated farmland soil was explored. Pioneer plants Cynodon dactylon and two material formulas (Steel slag (SS):pyrolusite (PY):ferrous sulfide (FS) = 3:3:2 or 1:2:8) were used in pot experiments. The DTPA method was used to extract the bioavailable heavy metals from soil, and then, the reduction rates of the bioavailable heavy metals were calculated. After harvesting plants, data of moisture content, biomass, root length and plant height were obtained. The remediation effect was evaluated according to the above indexes. The experimental results showed that the remediation effect of Bidentis pilosa was better than that of Cynodon dactylon. The addition of solid waste material significantly reduced the content of bioavailable Cd and As in soil by 97.73% and 53.54%, respectively. Suitable wastes may be a potential addition to heavy metal contaminated soils to promote phytoremediation of heavy metals.

Coordination of diverse individuals often requires sophisticated communications and high-order computational abilities. Microbial populations can exhibit diverse individualistic behaviors, and yet can engage in collective migratory patterns with a spatially sorted arrangement of phenotypes. However, it is unclear how such spatially sorted patterns emerge from diverse individuals without complex computational abilities. Here, by investigating the single-cell trajectories during group migration, we discovered that, despite the constant migrating speed of a group, the drift velocities of individual bacteria decrease from the back to the front. With a Langevin-type modeling framework, we showed that this decreasing profile of drift velocities implies the spatial modulation of individual run-and-tumble random motions, and enables the bacterial population to migrate as a pushed wave front. Theoretical analysis and stochastic simulations further predicted that the pushed wave front can help a diverse population to stay in a tight group, while diverse individuals perform the same type of mean reverting processes around centers orderly aligned by their chemotactic abilities. This mechanism about the emergence of orderly collective migration from diverse individuals is experimentally demonstrated by titration of bacterial chemoreceptor abundance. These results reveal a simple computational principle for emergent ordered behaviors from heterogeneous individuals.

Background Due to the COVID-19 outbreak, all teaching activities in nursing schools were suspended in China, and many nursing students were summoned to work in hospitals to compensate for the shortage of manpower. This study examined the prevalence of fatigue and its association with quality of life (QOL) among nursing students during the post-COVID-19 era in China. Methods This was a multicenter, cross-sectional study. Nursing students in five Chinese universities were invited to participate. Fatigue, depressive and anxiety symptoms, pain and QOL were measured using standardized instruments. Results A total of 1,070 nursing students participated. The prevalence of fatigue was 67.3% (95% CI [64.4–70.0]). Multiple logistic regression analysis revealed that male gender (P = 0.003, OR = 1.73, 95% CI [1.20–2.49]), and being a senior nursing student (second year: OR = 2.20, 95% CI [1.46–3.33], P < 0.001; third year: OR = 3.53, 95% CI [2.31–5.41], P < 0.001; and fourth year OR = 3.59, 95% CI [2.39–5.40], P < 0.001) were significantly associated with more severe fatigue. In addition, moderate economic loss during the COVID-19 pandemic (OR = 1.48, 95% CI [1.08–3.33], P < 0.015; compared to low loss), participants with more severe depressive (OR = 1.48, 95% CI [1.22–1.78], P < 0.001) and anxiety symptoms (OR = 1.12, 95% CI [1.05–1.20], P = 0.001), and more severe pain (OR = 1.67, 95%CI [1.46–1.91], P < 0.001) were significantly associated with reported more severe fatigue. After controlling for covariates, nursing students with fatigue had a lower overall QOL score compared to those without (F(1, 1070) = 31.4, P < 0.001). Conclusion Fatigue was common among nursing students in the post-COVID-19 era. Considering the negative impact of fatigue on QOL and daily functioning, routine physical and mental health screening should be conducted for nursing students. Effective stress-reduction measures should be enforced to assist this subpopulation to combat fatigue and restore optimal health.

Oxaliplatin, fluorouracil plus leucovorin (FOLFOX) regimen is the first-line chemotherapy of patients with metastatic colorectal cancer (mCRC). However, studies are limited regarding long non-coding RNAs (lncRNAs) associated with FOLFOX chemotherapy response and prognosis. This study aimed to identify lncRNAs associated with FOLFOX chemotherapy response and prognosis in mCRC patients and to construct a predictive model. We analyzed lncRNA expression in 11 mCRC patients treated with FOLFOX chemotherapy before surgery (four sensitive, seven resistant) by Gene Array Chip. The top eight lncRNAs (AC007193.8, CTD-2008N3.1, FLJ36777, RP11-509J21.4, RP3-508I15.20, LOC100130950, RP5-1042K10.13, and LINC00476) for chemotherapy response were identified according to weighted correlation network analysis (WGCNA). A competitive endogenous RNA (ceRNA) network was then constructed. The crucial functions of the eight lncRNAs enriched in chemotherapy resistance were mitogen-activated protein kinase (MAPK) and proteoglycans signaling pathway. Receiver operating characteristic (ROC) analysis demonstrated that the eight lncRNAs were potent predictors for chemotherapy resistance of mCRC patients. To further identify a signature model lncRNA chemotherapy response and prognosis, the validation set consisted of 196 CRC patients from our center was used to validate lncRNAs expression and prognosis by quantitative PCR (qPCR). The expression of the eight lncRNAs expression between CRC cancerous and adjacent non-cancerous tissues was also verified in the validation data set to determine the prognostic value. A generalized linear model was established to predict the probability of chemotherapy resistance and survival. Our findings showed that the eight-lncRNA signature may be a novel biomarker for the prediction of FOLFOX chemotherapy response and prognosis of mCRC patients.

Microbial dysbiosis in the upper digestive tract is linked to an increased risk of esophageal squamous cell carcinoma (ESCC). Overabundance of Porphyromonas gingivalis is associated with shorter survival of ESCC patients. We investigated the molecular mechanisms driving aggressive progression of ESCC by P. gingivalis. Intracellular invasion of P. gingivalis potentiated proliferation, migration, invasion, and metastasis abilities of ESCC cells via transforming growth factor-β (TGFβ)-dependent Drosophila mothers against decapentaplegic homologs (Smads)/Yes-associated protein (YAP)/Transcriptional coactivator with PDZ-binding motif (TAZ) activation. Smads/YAP/TAZ/TEA domain transcription factor1 (TEAD1) complex formation was essential to initiate downstream target gene expression, inducing an epithelial-mesenchymal transition (EMT) and stemness features. Furthermore, P. gingivalis augmented secretion and bioactivity of TGFβ through glycoprotein A repetitions predominant (GARP) up-regulation. Accordingly, disruption of either the GARP/TGFβ axis or its activated Smads/YAP/TAZ complex abrogated the tumor-promoting role of P. gingivalis. P. gingivalis signature genes based on its activated effector molecules can efficiently distinguish ESCC patients into low- and high-risk groups. Targeting P. gingivalis or its activated effectors may provide novel insights into clinical management of ESCC.

Summary: Histone methylation is essential for regulating gene expression during organogenesis to maintain stem cells and execute a proper differentiation program for their descendants. Here we show that the COMPASS family histone methyltransferase co-factor ASH2L is required for maintaining neural progenitor cells (NPCs) and the production and positioning of projection neurons during neocortex development. Specifically, loss of Ash2l in NPCs results in malformation of the neocortex; the mutant neocortex has fewer neurons, which are also abnormal in composition and laminar position. Moreover, ASH2L loss impairs trimethylation of H3K4 and the transcriptional machinery specific for Wnt-β-catenin signaling, inhibiting the proliferation ability of NPCs at late stages of neurogenesis by disrupting S phase entry to inhibit cell cycle progression. Overexpressing β-catenin after ASH2L elimination rescues the proliferation deficiency. Therefore, our findings demonstrate that ASH2L is crucial for modulating Wnt signaling to maintain NPCs and generate a full complement of neurons during mammalian neocortex development. : Precise orchestration of gene expression dynamics is essential for stem cells to execute a proper differentiation program during organogenesis. Li et al. demonstrate that ASH2L, a core subunit of the COMPASS methyltransferase complex, is critical for maintaining neural progenitor cells and the generation of different neuronal types during mammalian neocortical development. Keywords: ASH2L, COMPASS, Wnt signaling pathway, corticogenesis, H3K4me3, cell cycle, neurogenesis

The effects of Spartina alterniflora invasion on macrobenthos have long been of concern; however, there is currently no unified conclusion regarding these effects. Most studies on crabs focus on one species or limited habitat types, and assessments of the community-level effects of S. alterniflora invasion considering multiple species and habitat types have rarely been conducted. In this study, we sampled crabs along a habitat gradient from the shoreline to inland areas on the Yellow Sea coast, including the mudflat, S. alterniflora marsh, Suaeda salsa marsh and Phragmites australis marsh. A total of 10 crab species were found among all habitats, with five species in the mudflat, six species in S. alterniflora marsh, seven species in S. salsa marsh and four species in P. australis marsh. The Shannon index values for the crab communities were similar between S. alterniflora marsh and S. salsa marsh, and these values were significantly higher than those for the mudflat and P. australis marsh. However, the total biomass of crabs was highest in the mudflat, and Metaplax longipes, Philyra pisum and Macrophthalmus dilatatus exclusively preferred the mudflat. The analysis of principal components and similarities showed that the crab community structure in S. alterniflora marsh was most similar to that in S. salsa marsh, while the crab community structure in the mudflat was most different from that in the other habitat types. Our results demonstrate that the distribution of crabs varies across a habitat gradient after S. alterniflora invasion and that the crab community in S. alterniflora marsh is slightly different from that associated with the local vegetation but shows a large difference from that in the mudflat. This study indicates that some crab species may have adapted to habitat containing alien S. alterniflora, while other crab species reject this new marsh type. The effects of the distribution of crabs after S. alterniflora invasion on the regional ecosystem need further study in the future.

Human hepatitis B virus (HBV) infection and HBV-related diseases remain a major public health problem. Individuals coinfected with its satellite hepatitis D virus (HDV) have more severe disease. Cellular entry of both viruses is mediated by HBV envelope proteins. The pre-S1 domain of the large envelope protein is a key determinant for receptor(s) binding. However, the identity of the receptor(s) is unknown. Here, by using near zero distance photo-cross-linking and tandem affinity purification, we revealed that the receptor-binding region of pre-S1 specifically interacts with sodium taurocholate cotransporting polypeptide (NTCP), a multiple transmembrane transporter predominantly expressed in the liver. Silencing NTCP inhibited HBV and HDV infection, while exogenous NTCP expression rendered nonsusceptible hepatocarcinoma cells susceptible to these viral infections. Moreover, replacing amino acids 157–165 of nonfunctional monkey NTCP with the human counterpart conferred its ability in supporting both viral infections. Our results demonstrate that NTCP is a functional receptor for HBV and HDV.

Abstract Background The lengths of 5’UTRs of multicellular eukaryotes have been suggested to be subject to stochastic changes, with upstream start codons (uAUGs) as the major constraint to suppress 5’UTR elongation. However, this stochastic model cannot fully explain the variations in 5’UTR length. We hypothesize that the selection pressure on a combination of genomic features is also important for 5’UTR evolution. The ignorance of these features may have limited the explanatory power of the stochastic model. Furthermore, different selective constraints between vertebrates and invertebrates may lead to differences in the determinants of 5’UTR length, which have not been systematically analyzed. Methods Here we use a multiple linear regression model to delineate the correlation between 5’UTR length and the combination of a series of genomic features (G+C content, observed-to-expected (OE) ratios of uAUGs, upstream stop codons (uSTOPs), methylation-related CG/UG dinucleotides, and mRNA-destabilizing UU/UA dinucleotides) in six vertebrates (human, mouse, rat, chicken, African clawed frog, and zebrafish) and four invertebrates (fruit fly, mosquito, sea squirt, and nematode). The relative contributions of each feature to the variation of 5’UTR length were also evaluated. Results We found that 14%~33% of the 5’UTR length variations can be explained by a linear combination of the analyzed genomic features. The most important genomic features are the OE ratios of uSTOPs and G+C content. The surprisingly large weightings of uSTOPs highlight the importance of selection on upstream open reading frames (which include both uAUGs and uSTOPs), rather than on uAUGs per se. Furthermore, G+C content is the most important determinants for most invertebrates, but for vertebrates its effect is second to uSTOPs. We also found that shorter 5’UTRs are affected more by the stochastic process, whereas longer 5’UTRs are affected more by selection pressure on genomic features. Conclusions Our results suggest that upstream open reading frames may be the real target of selection, rather than uAUGs. We also show that the selective constraints on genomic features of 5’UTRs differ between vertebrates and invertebrates, and between longer and shorter 5’UTRs. A more comprehensive model that takes these findings into consideration is needed to better explain 5’UTR length evolution.

Abstract Background Organismal complexity is suggested to increase with the complexity of transcriptional and translational regulations. Supporting this notion is a recent study that demonstrated a higher level of tissue-specific gene expression in human than in mouse. However, whether this correlation can be extended beyond mammals remains unclear. In addition, 5' untranslated regions (5'UTRs), which have undergone stochastic elongation during evolution and potentially included an increased number of regulatory elements, may have played an important role in the emergence of organismal complexity. Although the lack of correlation between 5'UTR length and organismal complexity has been proposed, the underlying mechanisms remain unexplored. Results In this study, we select the number of cell types as the measurement of organismal complexity and examine the correlation between (1) organismal complexity and transcriptional regulatory complexity; and (2) organismal complexity and 5'UTR length by comparing the 5'UTRs and multiple-tissue expression profiles of human (Homo sapiens), mouse (Mus musculus), and fruit fly (Drosophila melanogaster). The transcriptional regulatory complexity is measured by using the tissue specificity of gene expression and the ratio of non-constitutively expressed to constitutively expressed genes. We demonstrate that, whereas correlation (1) holds well in the three-way comparison, correlation (2) is not true. Results from a larger dataset that includes more than 15 species, ranging from yeast to human, also reject correlation (2). The reason for the failure of correlation (2) may be ascribed to: Firstly, longer 5'UTRs do not contribute to increased tissue specificity of gene expression. Secondly, the increased numbers of common translational regulatory elements in longer 5'UTRs do not lead to increased organismal complexity. Conclusions Our study has extended the evidence base for the correlation between organismal complexity and transcriptional regulatory complexity from mammals to fruit fly, the representative model organism of invertebrates. Furthermore, our results suggest that the elongation of 5'UTRs alone can not lead to the increase in regulatory complexity or the emergence of organismal complexity.

Abstract Background High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. Results In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. Conclusions Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode.

Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer), to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.